2HNT

CRYSTALLOGRAPHIC STRUCTURE OF HUMAN GAMMA-THROMBIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystallographic structure of human gamma-thrombin.

Rydel, T.J., Yin, M., Padmanabhan, K.P., Blankenship, D.T., Cardin, A.D., Correa, P.E., Fenton 2nd., J.W., Tulinsky, A.

(1994) J Biol Chem 269: 22000-22006

  • Primary Citation of Related Structures:  
    2HNT

  • PubMed Abstract: 

    • In an effort to prepare crystals and determine the structure of alpha-thrombin complexed to a synthetic peptide inhibitor (MDL-28050) of the hirudin 54-65 COOH-terminal region, it was discovered that the crystals were not those of the complex but of gamma-thrombin ...

    In an effort to prepare crystals and determine the structure of alpha-thrombin complexed to a synthetic peptide inhibitor (MDL-28050) of the hirudin 54-65 COOH-terminal region, it was discovered that the crystals were not those of the complex but of gamma-thrombin. Gel electrophoresis studies revealed that autolytic degradation had occurred prior to crystallization. NH2-terminal sequence analysis of these autolytic fragments confirmed the gamma-thrombin product (cleavages at Arg75-Tyr76 and/or Arg77A-Asn78, and Lys149E-Gly150; chymotrypsinogen numbering) with a minor amount of another autolysis product, beta-thrombin (first two cleavages only). The final structure has an R-factor of 0.156 for 7.0-2.5-A data, and includes 186 water molecules. A comparison of gamma-thrombin with the thrombin structure in the alpha-thrombin-hirugen complex revealed that the two structures agreed well (r.m.s. delta = 0.39 A for main chain atoms). These structures possess uninhibited active sites where the disposition of the catalytic triad residues is nearly identical. The electron density in the vicinity of the gamma-thrombin cleavage regions is poor, and only becomes well-defined several residues prior to and after the actual cleavage sites. The extensive disorder evoked by beta-cleavage(s) in the Lys70-Glu80 loop region indicates that this part of the molecule is severely disrupted by autolysis and is the reason exosite functions are dramatically impaired in beta-and gamma-thrombin. Since autolysis did not lead to a major reorganization of the folded structure of alpha-thrombin, the likely structural features of the interaction of thrombin substrate with thrombin enzyme during beta-cleavage have been modeled by docking the exosite region of one molecule at the active site of another.

    Related Citations: 
    • Refined Structure of the Hirudin-Thrombin Complex
      Rydel, T.J., Tulinsky, A., Bode, W., Huber, R.
      (1991) J Mol Biol 221: 583
    • Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin
      Skrzypczak-Jankun, E., Carperos, V.E., Ravichandran, K.G., Tulinsky, A., Westbrook, M., Maraganore, J.M.
      (1991) J Mol Biol 221: 1379
    Organizational Affiliation: 

    Department of Chemistry, Michigan State University, East Lansing 48824-1322.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GAMMA-THROMBINA [auth L]36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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Go to UniProtKB:  P00734
PHAROS:  P00734
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UniProt GroupP00734
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GAMMA-THROMBINB [auth C]70Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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PHAROS:  P00734
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UniProt GroupP00734
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GAMMA-THROMBINC [auth E]81Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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UniProt GroupP00734
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
GAMMA-THROMBIND [auth F]105Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
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UniProt GroupP00734
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.45α = 90
b = 48.23β = 96.2
c = 52.43γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1994-08-23 
  • Released Date: 1994-11-30 
    • Deposition Author(s): Tulinsky, A.

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance